The message you receive when making a site joinable:
"Important: People who join your site can access the materials on your site. Sites with sensitive materials should not be made joinable."
This message is using the "messageValidation" class, which now makes it look like an error. In our institution's flavour of Sakai, we changed this to the "messageWarning" class, but this class was removed from reference's tool_base.css for whatever reason.
The linked PR reintroduces this class to tool_base.css, and changes the class on the element in chef_site-siteInfo-editAccess.vm.